plated through holes (PTH) are holes that are placed on drill layer while non-plated through holes (NPTH) are placed on outline layers
This is a bit tricky on KiCAD as it will produce two NC drill files for PTH and NPTH holes. For some who don't care about non plated through holes, they combine the two drill file using gerbMerge as one all plated holes. A workaround for this is manually draw a hole and place it on the outline layer.